(ahem) ok, basically i'd say it helps you to organize addons. This is good if you have, say, 800 addons in your ../Flashpoint/Addons folder, because at gamestart all Addons are loaded into your free RAM / registered ingame to be 'valid'. So, the more Addons you have to less RAM you have left for playing OpF. Which is bad - sometimes you get the message: "Can't load o.pbo into memory" or something like that. This is directly connected to a low amount of free RAM.
By placing certain Addons in certain Modfolders you can make OpF load only the Addons in the modfolder and of course, all addons in the normal Addon folders (/OpFlashpoint/Addons/ and /OpFlashpoint/Res/Addons/).
So it makes sense to make different modfolders that follow a certain theme: Vietnam, WorldWar2, DesertConflict, SnowThemed, etc etc.
Then you put the appropiate addons into these modfolders:
SebNampack2 into Modfolder '../OpFlashpoint/Vietnam/Addons/' for example.
To start activate a certain modfolder, copy & edit different links which start your OpF Resistance with the appropiate '-mod:xxx' parameter: you could start with a Vietnam themed OpF (-mod:Vietnam), a Desert OpF (Modfolder 'Desert' for example), a WorldWar2 OpF ('WW2' folder) etc etc...
That way OpF won't waste RAM space by loading desert, ww2, and other addons together with the vietnam addons.
Still not the answer you wanted ? Plz ask a bit more precisely...